DESCRIPTION

g_covar calculates and diagonalizes the (mass-weighted) covariance matrix. All structures are fitted to the structure in the structure file. When this is not a run input file periodicity will not be taken into account. When the fit and analysis groups are identical and the analysis is non mass-weighted, the fit will also be non mass-weighted.

The eigenvectors are written to a trajectory file ( -v). When the same atoms are used for the fit and the covariance analysis, the reference structure for the fit is written first with t=-1. The average (or reference when -ref is used) structure is written with t=0, the eigenvectors are written as frames with the eigenvector number as timestamp.

The eigenvectors can be analyzed with g_anaeig.

Option -ascii writes the whole covariance matrix to an ASCII file. The order of the elements is: x1x1, x1y1, x1z1, x1x2, ...

Option -xpm writes the whole covariance matrix to an xpm file.

Option -xpma writes the atomic covariance matrix to an xpm file, i.e. for each atom pair the sum of the xx, yy and zz covariances is written.

FILES

-ftraj.xtcInput Trajectory: xtc trr trj gro g96 pdb cpt

-stopol.tprInput Structure+mass(db): tpr tpb tpa gro g96 pdb

-nindex.ndxInput, Opt. Index file

-oeigenval.xvgOutput xvgr/xmgr file

-veigenvec.trrOutput Full precision trajectory: trr trj cpt

-avaverage.pdbOutput Structure file: gro g96 pdb etc.

-lcovar.logOutput Log file

-asciicovar.datOutput, Opt. Generic data file

-xpmcovar.xpmOutput, Opt. X PixMap compatible matrix file

-xpmacovara.xpmOutput, Opt. X PixMap compatible matrix file

OTHER OPTIONS

-[no]hno Print help info and quit

-[no]versionno Print version info and quit

-niceint19 Set the nicelevel

-btime0 First frame (ps) to read from trajectory

-etime0 Last frame (ps) to read from trajectory

-dttime0 Only use frame when t MOD dt = first time (ps)

-tuenumps Time unit: fs, ps, ns, us, ms or s

-xvgenumxmgrace xvg plot formatting: xmgrace, xmgr or none

-[no]fityes Fit to a reference structure

-[no]refno Use the deviation from the conformation in the structure file instead of from the average